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| Status |
Public on Mar 25, 2023 |
| Title |
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.
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| Overall design |
Using a standardized nucleus extraction method, single-nucleus RNA seq was performed on whole Arabidopsis organs and tissues, including seeds, seedlings, rosettes, stems, flowers, and siliques, at ten developmental timepoints throughout the entire lifecycle of the plant. A minimum of four single-nucleus RNA-seq runs were performed per tissue and timepoint.
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| Web link |
http://DOI: 10.1038/s41477-025-02072-z
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| Contributor(s) |
Lee TA, Nobori T, Illouz-Eliaz N, Jow B, Nery JR, Ecker JR |
| Citation(s) |
40830271 |
| |
| Submission date |
Feb 24, 2023 |
| Last update date |
Aug 29, 2025 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
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| Phone |
8584534100
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| Organization name |
HHMI-Salk-Institute
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| Department |
Genomic Analysis Laboratory
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| Lab |
Ecker lab
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| Street address |
10010 North Torrey Pines Road
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (84)
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| GSM7063664 |
0-day-old imbibed seeds, run 1, snRNA-seq |
| GSM7063665 |
0-day-old imbibed seeds, run 2, snRNA-seq |
| GSM7063666 |
0-day-old imbibed seeds, run 3, snRNA-seq |
| GSM7063667 |
0-day-old imbibed seeds, run 4, snRNA-seq |
| GSM7063668 |
Flowers, run 1, snRNA-seq |
| GSM7063669 |
Flowers, run 2, snRNA-seq |
| GSM7063670 |
Flowers, run 3, snRNA-seq |
| GSM7063671 |
Flowers, run 4, snRNA-seq |
| GSM7063672 |
Flowers, run 5, snRNA-seq |
| GSM7063673 |
Flowers, run 6, snRNA-seq |
| GSM7063674 |
30-day-old rosette, run 1, snRNA-seq |
| GSM7063675 |
30-day-old rosette, run 2, snRNA-seq |
| GSM7063676 |
30-day-old rosette, run 3, snRNA-seq |
| GSM7063677 |
30-day-old rosette, run 4, snRNA-seq |
| GSM7063678 |
30-day-old rosette, run 5, snRNA-seq |
| GSM7063679 |
30-day-old rosette, run 6, snRNA-seq |
| GSM7063680 |
21-day-old rosette, run 1, snRNA-seq |
| GSM7063681 |
21-day-old rosette, run 2, snRNA-seq |
| GSM7063682 |
21-day-old rosette, run 3, snRNA-seq |
| GSM7063683 |
21-day-old rosette, run 4, snRNA-seq |
| GSM7063684 |
21-day-old rosette, run 5, snRNA-seq |
| GSM7063685 |
21-day-old rosette, run 6, snRNA-seq |
| GSM7063686 |
21-day-old rosette, run 7, snRNA-seq |
| GSM7063687 |
21-day-old rosette, run 8, snRNA-seq |
| GSM7063688 |
44-day-old silique, run 1, snRNA-seq |
| GSM7063689 |
44-day-old silique, run 2, snRNA-seq |
| GSM7063690 |
44-day-old silique, run 3, snRNA-seq |
| GSM7063691 |
44-day-old silique, run 4, snRNA-seq |
| GSM7063692 |
44-day-old silique, run 5, snRNA-seq |
| GSM7063693 |
44-day-old silique, run 6, snRNA-seq |
| GSM7063694 |
44-day-old silique, run 7, snRNA-seq |
| GSM7063695 |
44-day-old silique, run 8, snRNA-seq |
| GSM7063696 |
1.25-day-old seeds, run 1, snRNA-seq |
| GSM7063697 |
1.25-day-old seeds, run 2, snRNA-seq |
| GSM7063698 |
1.25-day-old seeds, run 3, snRNA-seq |
| GSM7063699 |
1.25-day-old seeds, run 4, snRNA-seq |
| GSM7063700 |
1.25-day-old seeds, run 5, snRNA-seq |
| GSM7063701 |
1.25-day-old seeds, run 6, snRNA-seq |
| GSM7063702 |
40-day-old branched stem, run 1, snRNA-seq |
| GSM7063703 |
40-day-old branched stem, run 2, snRNA-seq |
| GSM7063704 |
40-day-old branched stem, run 3, snRNA-seq |
| GSM7063705 |
40-day-old basal stem and brached stem, run 1, CellPlex snRNA-seq |
| GSM7063706 |
40-day-old basal stem and brached stem, run 2, CellPlex snRNA-seq |
| GSM7063707 |
40-day-old basal stem, run 1, snRNA-seq |
| GSM7063708 |
40-day-old basal stem, run 2, snRNA-seq |
| GSM7063709 |
40-day-old apical stem, run 1, snRNA-seq |
| GSM7063710 |
40-day-old apical stem, run 2, snRNA-seq |
| GSM7063711 |
40-day-old apical stem, run 3, snRNA-seq |
| GSM7063712 |
40-day-old apical stem, run 1, CellPlex snRNA-seq |
| GSM7063713 |
40-day-old apical stem, run 2, CellPlex snRNA-seq |
| GSM7063714 |
40-day-old apical stem, run 3, CellPlex snRNA-seq |
| GSM7063715 |
12-day-old seedlings, run 10, snRNA-seq |
| GSM7063716 |
12-day-old seedlings, run 1, snRNA-seq |
| GSM7063717 |
12-day-old seedlings, run 11, snRNA-seq |
| GSM7063718 |
12-day-old seedlings, run 12, snRNA-seq |
| GSM7063719 |
12-day-old seedlings, run 13, snRNA-seq |
| GSM7063720 |
12-day-old seedlings, run 14, snRNA-seq |
| GSM7063721 |
12-day-old seedlings, run 15, snRNA-seq |
| GSM7063722 |
12-day-old seedlings, run 16, snRNA-seq |
| GSM7063723 |
12-day-old seedlings, run 17, snRNA-seq |
| GSM7063724 |
12-day-old seedlings, run 18, snRNA-seq |
| GSM7063725 |
12-day-old seedlings, run 19, snRNA-seq |
| GSM7063726 |
12-day-old seedlings, run 20, snRNA-seq |
| GSM7063727 |
12-day-old seedlings, run 2, snRNA-seq |
| GSM7063728 |
12-day-old seedlings, run 21, snRNA-seq |
| GSM7063729 |
12-day-old seedlings, run 22, snRNA-seq |
| GSM7063730 |
12-day-old seedlings, run 3, snRNA-seq |
| GSM7063731 |
12-day-old seedlings, run 4, snRNA-seq |
| GSM7063732 |
12-day-old seedlings, run 5, snRNA-seq |
| GSM7063733 |
12-day-old seedlings, run 6, snRNA-seq |
| GSM7063734 |
12-day-old seedlings, run 7, snRNA-seq |
| GSM7063735 |
12-day-old seedlings, run 8, snRNA-seq |
| GSM7063736 |
12-day-old seedlings, run 9, snRNA-seq |
| GSM7063737 |
3-day-old seedlings, run 1, snRNA-seq |
| GSM7063738 |
3-day-old seedlings, run 2, snRNA-seq |
| GSM7063739 |
3-day-old seedlings, run 3, snRNA-seq |
| GSM7063740 |
3-day-old seedlings, run 4, snRNA-seq |
| GSM7063741 |
6-day-old seedlings, run 1, snRNA-seq |
| GSM7063742 |
6-day-old seedlings, run 2, snRNA-seq |
| GSM7063743 |
6-day-old seedlings, run 3, snRNA-seq |
| GSM7063744 |
6-day-old seedlings, run 4, snRNA-seq |
| GSM7063745 |
6-day-old seedlings, run 5, snRNA-seq |
| GSM7063746 |
6-day-old seedlings, run 6, snRNA-seq |
| GSM7063747 |
1.25do seeds, Curio slide-seq |
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| Relations |
| BioProject |
PRJNA938501 |
| SRA |
SRP424479 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE226097_221121_curio_seed_seurat.rds.gz |
222.8 Mb |
(ftp)(http) |
RDS |
| GSE226097_flower_250805.rds |
1.1 Gb |
(ftp)(http) |
RDS |
| GSE226097_flower_relaxed_220706.rds |
64.7 Mb |
(ftp)(http) |
RDS |
| GSE226097_global_integration_221009.rds |
3.0 Gb |
(ftp)(http) |
RDS |
| GSE226097_hook_Col_hls1_integrated_250221.rds |
707.0 Mb |
(ftp)(http) |
RDS |
| GSE226097_relaxed_global_integration_221122.rds |
2.6 Gb |
(ftp)(http) |
RDS |
| GSE226097_rosette_21d_230221.rds.gz |
582.6 Mb |
(ftp)(http) |
RDS |
| GSE226097_rosette_21d_relaxed_220713.rds |
131.0 Mb |
(ftp)(http) |
RDS |
| GSE226097_rosette_30d_230221.rds.gz |
890.3 Mb |
(ftp)(http) |
RDS |
| GSE226097_rosette_30d_relaxed_220706.rds |
185.5 Mb |
(ftp)(http) |
RDS |
| GSE226097_rosette_merge_220824.rds |
355.3 Mb |
(ftp)(http) |
RDS |
| GSE226097_seed_0d_230221.rds.gz |
308.7 Mb |
(ftp)(http) |
RDS |
| GSE226097_seed_0d_relaxed_220711.rds |
87.0 Mb |
(ftp)(http) |
RDS |
| GSE226097_seed_125d_250805.rds |
8.2 Gb |
(ftp)(http) |
RDS |
| GSE226097_seed_125d_relaxed_220712.rds |
478.4 Mb |
(ftp)(http) |
RDS |
| GSE226097_seedling_12d_230221.rds.gz |
2.1 Gb |
(ftp)(http) |
RDS |
| GSE226097_seedling_12d_relaxed_220712.rds |
336.1 Mb |
(ftp)(http) |
RDS |
| GSE226097_seedling_3d_250805.rds |
1.3 Gb |
(ftp)(http) |
RDS |
| GSE226097_seedling_3d_relaxed_220711.rds |
58.9 Mb |
(ftp)(http) |
RDS |
| GSE226097_seedling_6d_230221.rds.gz |
1.2 Gb |
(ftp)(http) |
RDS |
| GSE226097_seedling_6d_relaxed_220710.rds |
136.7 Mb |
(ftp)(http) |
RDS |
| GSE226097_seedling_merge_220714.rds |
799.3 Mb |
(ftp)(http) |
RDS |
| GSE226097_silique_230221.rds.gz |
2.0 Gb |
(ftp)(http) |
RDS |
| GSE226097_silique_relaxed_220710.rds |
508.1 Mb |
(ftp)(http) |
RDS |
| GSE226097_spatial_dataset_flower_region1_250425.rds |
3.2 Mb |
(ftp)(http) |
RDS |
| GSE226097_spatial_dataset_flower_region2_250425.rds |
2.4 Mb |
(ftp)(http) |
RDS |
| GSE226097_spatial_dataset_flower_region2_long_250425.rds |
2.0 Mb |
(ftp)(http) |
RDS |
| GSE226097_stem_250805.rds |
1.6 Gb |
(ftp)(http) |
RDS |
| GSE226097_stem_relaxed_220706.rds |
92.3 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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